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Genome-wide association study

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https://www.readbyqxmd.com/read/29684485/dysregulation-of-fibrosis-related-genes-in-hcv-induced-liver-disease
#1
Reham M Dawood, Mai Abd El-Meguid, Marwa K Ibrahim, Noha G Bader El Din, Ahmed Barakat, Khaled El-Wakeel, Mohamed Darwish Ahmed Abd Alla, George Y Wu, Mostafa K El Awady
BACKGROUND: Liver fibrosis results from a wound healing response to chronic injury, which leads to excessive matrix deposition. Genome wide association studies have showen transcriptional dysregulation in mild and severe liver fibrosis. Recent studies suggested that genetic markers may be able to define the exact stage of liver fibrosis. AIM: To define genes or genetic pathways that could serve as markers for staging or as therapeutic targets to halt progression of liver fibrosis...
April 20, 2018: Gene
https://www.readbyqxmd.com/read/29684110/mechanistic-insights-into-anticancer-properties-of-oligomeric-proanthocyanidins-from-grape-seeds-in-colorectal-cancer
#2
Preethi Ravindranathan, Divya Pasham, Uthra Balaji, Jacob Cardenas, Jinghua Gu, Shusuke Toden, Ajay Goel
Although the anticancer properties of oligomeric proanthocyanidins (OPCs) from grape seeds have been well recognized, the molecular mechanisms by which they exert anticancer effects are poorly understood. In this study, through comprehensive RNA-sequencing-based gene expression profiling in multiple colorectal cancer cell lines, we for the first time illuminate the genome-wide effects of OPCs from grape seeds in colorectal cancer. Our data revealed that OPCs affect several key cancer-associated genes. In particular, genes involved in cell cycle and DNA replication were most significantly and consistently altered by OPCs across multiple cell lines...
April 19, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29684019/one-for-all-and-all-for-one-improving-replication-of-genetic-studies-through-network-diffusion
#3
Daniel Lancour, Adam Naj, Richard Mayeux, Jonathan L Haines, Margaret A Pericak-Vance, Gerard C Schellenberg, Mark Crovella, Lindsay A Farrer, Simon Kasif
Improving accuracy in genetic studies would greatly accelerate understanding the genetic basis of complex diseases. One approach to achieve such an improvement for risk variants identified by the genome wide association study (GWAS) approach is to incorporate previously known biology when screening variants across the genome. We developed a simple approach for improving the prioritization of candidate disease genes that incorporates a network diffusion of scores from known disease genes using a protein network and a novel integration with GWAS risk scores, and tested this approach on a large Alzheimer disease (AD) GWAS dataset...
April 23, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29683462/polysome-profiling-in-leishmania-human-cells-and-mouse-testis
#4
Zemfira N Karamysheva, Elena B Tikhonova, Petar N Grozdanov, James C Huffman, Kristen R Baca, Alexander Karamyshev, R Brian Denison, Clinton C MacDonald, Kai Zhang, Andrey L Karamyshev
Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For a long time, the gene expression studies were dominated by research on the transcriptional level. However, the steady-state levels of mRNAs do not correlate well with protein production, and the translatability of mRNAs varies greatly depending on the conditions. In some organisms, like the parasite Leishmania, the protein expression is regulated mostly at the translational level...
April 8, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29682886/a-common-regulatory-variant-in-slc35b4-influences-the-recurrence-and-survival-of-prostate-cancer
#5
Eric Y Huang, Yu-Jia Chang, Shu-Pin Huang, Victor C Lin, Chia-Cheng Yu, Chao-Yuan Huang, Hsin-Ling Yin, Ta-Yuan Chang, Te-Ling Lu, Bo-Ying Bao
Single nucleotide polymorphisms (SNPs) within the regulatory elements of a gene can alter gene expression, making these SNPs of prime importance for candidate gene association studies. We aimed to determine whether such regulatory variants are associated with clinical outcomes in three cohorts of patients with prostate cancer. We used RegulomeDB to identify potential regulatory variants based on in silico predictions and reviewed genome-wide experimental findings. Overall, 131 putative regulatory SNPs with the highest confidence score on predicted functionality were investigated in two independent localized prostate cancer cohorts totalling 458 patients who underwent radical prostatectomy...
April 23, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29682858/natural-biological-variation-of-white-matter-microstructure-is-accentuated-in-huntington-s-disease
#6
Sarah Gregory, Helen Crawford, Kiran Seunarine, Blair Leavitt, Alexandra Durr, Raymund A C Roos, Rachael I Scahill, Sarah J Tabrizi, Geraint Rees, Douglas Langbehn, Michael Orth
Huntington's disease (HD) is a monogenic neurodegenerative disorder caused by a CAG-repeat expansion in the Huntingtin gene. Presence of this expansion signifies certainty of disease onset, but only partly explains age at which onset occurs. Genome-wide association studies have shown that naturally occurring genetic variability influences HD pathogenesis and disease onset. Investigating the influence of biological traits in the normal population, such as variability in white matter properties, on HD pathogenesis could provide a complementary approach to understanding disease modification...
April 22, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/29682839/investigating-genetic-correlations-and-causal-effects-between-caffeine-consumption-and-sleep-behaviours
#7
Jorien L Treur, Mark Gibson, Amy E Taylor, Peter J Rogers, Marcus R Munafò
Observationally, higher caffeine consumption is associated with poorer sleep and insomnia. We investigated whether these associations are a result of shared genetic risk factors and/or (possibly bidirectional) causal effects. Summary-level data were available from genome-wide association studies on caffeine intake (n = 91 462), plasma caffeine and caffeine metabolic rate (n = 9876), sleep duration and chronotype (being a "morning" versus an "evening" person) (n = 128 266), and insomnia complaints (n = 113 006)...
April 22, 2018: Journal of Sleep Research
https://www.readbyqxmd.com/read/29682794/genetic-associations-with-childhood-brain-growth-defined-in-two-longitudinal-cohorts
#8
Eszter Szekely, Tae-Hwi Linus Schwantes-An, Cristina M Justice, Jeremy A Sabourin, Philip R Jansen, Ryan L Muetzel, Wendy Sharp, Henning Tiemeier, Heejong Sung, Tonya J White, Alexander F Wilson, Philip Shaw
Genome-wide association studies (GWASs) are unraveling the genetics of adult brain neuroanatomy as measured by cross-sectional anatomic magnetic resonance imaging (aMRI). However, the genetic mechanisms that shape childhood brain development are, as yet, largely unexplored. In this study we identify common genetic variants associated with childhood brain development as defined by longitudinal aMRI. Genome-wide single nucleotide polymorphism (SNP) data were determined in two cohorts: one enriched for attention-deficit/hyperactivity disorder (ADHD) (LONG cohort: 458 participants; 119 with ADHD) and the other from a population-based cohort (Generation R: 257 participants)...
April 22, 2018: Genetic Epidemiology
https://www.readbyqxmd.com/read/29682782/a-hierarchical-clustering-method-for-dimension-reduction-in-joint-analysis-of-multiple-phenotypes
#9
Xiaoyu Liang, Qiuying Sha, Yeonwoo Rho, Shuanglin Zhang
Genome-wide association studies (GWAS) have become a very effective research tool to identify genetic variants of underlying various complex diseases. In spite of the success of GWAS in identifying thousands of reproducible associations between genetic variants and complex disease, in general, the association between genetic variants and a single phenotype is usually weak. It is increasingly recognized that joint analysis of multiple phenotypes can be potentially more powerful than the univariate analysis, and can shed new light on underlying biological mechanisms of complex diseases...
April 22, 2018: Genetic Epidemiology
https://www.readbyqxmd.com/read/29682616/human-ccl3l1-copy-number-variation-gene-expression-and-the-role-of-the-ccl3l1-ccr5-axis-in-lung-function
#10
Adeolu B Adewoye, Nick Shrine, Linda Odenthal-Hesse, Samantha Welsh, Anders Malarstig, Scott Jelinsky, Iain Kilty, Martin D Tobin, Edward J Hollox, Louise V Wain
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29682093/dna-methylation-in-osteoarthritis-current-status-and-therapeutic-implications
#11
REVIEW
Antonio Miranda-Duarte
Background: Primary Osteoarthritis (OA) is a multifactorial disease in which genetic factors are strongly associated with its development; however, recently it has been observed that epigenetic modifications are also involved in the pathogenesis of OA. DNA methylation is related to gene silencing, and several studies have investigated its role in the loci of different pathways or molecules associated to OA. Objective: This review is focused on the current status of DNA methylation studies related to OA pathogenesis...
2018: Open Rheumatology Journal
https://www.readbyqxmd.com/read/29681884/glutathione-s-transferase-alpha-4-prevents-dopamine-neurodegeneration-in-a-rat-alpha-synuclein-model-of-parkinson-s-disease
#12
Michael Jewett, Elna Dickson, Kajsa Brolin, Matilde Negrini, Itzia Jimenez-Ferrer, Maria Swanberg
Parkinson's disease (PD) is a common, progressive neurodegenerative disease, which typically presents itself with a range of motor symptoms, like resting tremor, bradykinesia, and rigidity, but also non-motor symptoms such as fatigue, constipation, and sleep disturbance. Neuropathologically, PD is characterized by loss of dopaminergic cells in the substantia nigra pars compacta (SNpc) and Lewy bodies, neuronal inclusions containing α-synuclein (α-syn). Mutations and copy number variations of SNCA , the gene encoding α-syn, are linked to familial PD and common SNCA gene variants are associated to idiopathic PD...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/29681852/genotypic-and-phenotypic-factors-influencing-drug-response-in-mexican-patients-with-type-2-diabetes-mellitus
#13
Hector E Sanchez-Ibarra, Luisa M Reyes-Cortes, Xian-Li Jiang, Claudia M Luna-Aguirre, Dionicio Aguirre-Trevino, Ivan A Morales-Alvarado, Rafael B Leon-Cachon, Fernando Lavalle-Gonzalez, Faruck Morcos, Hugo A Barrera-Saldaña
The treatment of Type 2 Diabetes Mellitus (T2DM) consists primarily of oral antidiabetic drugs (OADs) that stimulate insulin secretion, such as sulfonylureas (SUs) and reduce hepatic glucose production (e.g., biguanides), among others. The marked inter-individual differences among T2DM patients' response to these drugs have become an issue on prescribing and dosing efficiently. In this study, fourteen polymorphisms selected from Genome-wide association studies (GWAS) were screened in 495 T2DM Mexican patients previously treated with OADs to find the relationship between the presence of these polymorphisms and response to the OADs...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29681542/dna-methylation-and-regulatory-elements-during-chicken-germline-stem-cell-differentiation
#14
Yanghua He, Qisheng Zuo, John Edwards, Keji Zhao, Jinzhi Lei, Wentao Cai, Qing Nie, Bichun Li, Jiuzhou Song
The production of germ cells in vitro would open important new avenues for stem biology and human medicine, but the mechanisms of germ cell differentiation are not well understood. The chicken, as a great model for embryology and development, was used in this study to help us explore its regulatory mechanisms. In this study, we reported a comprehensive genome-wide DNA methylation landscape in chicken germ cells, and transcriptomic dynamics was also presented. By uncovering DNA methylation patterns on individual genes, some genes accurately modulated by DNA methylation were found to be associated with cancers and virus infection, e...
April 17, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29680088/clustered-regularly-interspaced-short-palindromic-repeat-crispr-crispr-associated-endonuclease-cas9-mediated-homology-independent-integration-for-generating-quality-control-materials-for-clinical-molecular-genetic-testing
#15
Guigao Lin, Kuo Zhang, Rongxue Peng, Yanxi Han, Jiehong Xie, Jinming Li
Genome-edited human cell lines are important resources for producing quality control materials for clinical molecular genetic testing. Generating cell lines with defined mutations through homology-directed repair-based methods are inefficient and can lead to unwanted insertions and deletions in the target loci. Nonhomologous end joining in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease Cas9 (Cas9) system was harnessed to generate genome-engineered cell lines harboring target mutations...
May 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29679879/polygenic-risk-score-of-serpina6-serpina1-associates-with-diurnal-and-stress-induced-hpa-axis-activity-in-children
#16
Siddheshwar Utge, Katri Räikkönen, Eero Kajantie, Jari Lipsanen, Sture Andersson, Timo Strandberg, Rebecca M Reynolds, Johan G Eriksson, Jari Lahti
PURPOSE: Corticosteroid-binding globulin (CBG) transports glucocorticoids in blood. Variation in genes SERPINA6 encoding for CBG, SERPINA2 and SERPINA1 (serpin family A member 6, 2, and 1) have been shown to influence morning plasma cortisol and CBG in adults. However, association of this genetic variation with diurnal and stress-induced salivary cortisol remain unknown. This study aims to investigate the effect of genetic variation in SERPINA6/2/1 loci on diurnal and stress-induced salivary cortisol in children...
April 13, 2018: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/29679657/eleven-loci-with-new-reproducible-genetic-associations-with-allergic-disease-risk
#17
Manuel Ar Ferreira, Judith M Vonk, Hansjörg Baurecht, Ingo Marenholz, Chao Tian, Joshua D Hoffman, Quinta Helmer, Annika Tillander, Vilhelmina Ullemar, Yi Lu, Franz Rüschendorf, David A Hinds, Norbert Hübner, Stephan Weidinger, Patrik Ke Magnusson, Eric Jorgenson, Young-Ae Lee, Dorret I Boomsma, Robert Karlsson, Catarina Almqvist, Gerard H Koppelman, Lavinia Paternoster
BACKGROUND: A recent genome-wide association study (GWAS) identified 99 loci that contain genetic risk variants shared between asthma, hay fever and eczema. Many more risk loci shared between these common allergic diseases remain to be discovered, which could point to new therapeutic opportunities. OBJECTIVE: To identify novel risk loci shared between asthma, hay fever and eczema by applying a gene-based test of association to results from a published GWAS that included data from 360,838 individuals...
April 18, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29678584/genome-wide-profiles-of-metastasis-associated-mrnas-and-micrornas-in-salivary-adenoid-cystic-carcinoma
#18
Shubin Wang, Lei Zhang, Pengwei Shi, Yuanyuan Zhang, Hong Zhou, Xuanping Cao
Salivary adenoid cystic carcinoma (SACC) is often accompanied with poor prognosis due to local recurrence, distant metastasis, and perineural invasion. The mechanism involved in SACC metastasis is not yet fully understood. In this study, we profiled the expression of messenger RNA (mRNA) and microRNA (miRNA) in an SACC cell line, ACC-2, and a highly metastatic SACC cell line, ACC-M, using high-throughput sequencing. We discovered that: (1) differentially expressed (DE) mRNAs and DE miRNAs are potentially involved in SACC metastasis; (2) multiple regulatory interactions between DE miRNAs and DE mRNAs exist; and (3) miR-338-5p/3p target LAMC2 to impair motility and invasion of ACC-M and MDA-MB-231 cells...
April 17, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29677560/effective-discovery-of-rare-variants-by-pooled-target-capture-sequencing-a-comparative-analysis-with-individually-indexed-target-capture-sequencing
#19
Seungjin Ryu, Jeehae Han, Trina M Norden-Krichmar, Nicholas J Schork, Yousin Suh
Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies...
March 30, 2018: Mutation Research
https://www.readbyqxmd.com/read/29677463/a-role-for-collagen-iv-in-cardiovascular-disease
#20
Lasse Bach Steffensen, Lars M Rasmussen
Over the past decade, studies have repeatedly found single nucleotide polymorphisms located in the COL4A1 and COL4A2 genes to be associated with cardiovascular disease (CVD), and the 13q34 locus harboring these genes is one of approximately 160 genome-wide significant risk loci for coronary artery disease. COL4A1 and COL4A2 encode the ⍺1- and ⍺2-chains of collagen IV, a major component of basement membranes in various tissues including arteries. In spite of the growing body of evidence indicating a role for collagen IV in CVD, remarkably few studies aim at directly investigating such a role...
April 20, 2018: American Journal of Physiology. Heart and Circulatory Physiology
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